Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)

14 files changed, 106 insertions, 125 deletions

diff --git a/biology/ugene/files/patch-git_279756e4 b/biology/ugene/files/patch-git_279756e4
deleted file mode 100644
index f730ce8fe3c4..000000000000
--- a/biology/ugene/files/patch-git_279756e4
+++ /dev/null
@@ -1,30 +0,0 @@
-From 279756e448f53af5a495a2ce3a12abdf833fc703 Mon Sep 17 00:00:00 2001
-From: Kevin Kofler <kevin.kofler@chello.at>
-Date: Tue, 2 Jan 2018 22:21:03 +0100
-Subject: [PATCH] Fix build against Qt 5.10
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui: Remove
-shortcut setting that breaks the build with Qt 5.10.
-
-UGENE can be built with Qt ≥ 5.6 and a separate QtWebKit. With Qt 5.10,
-we were hitting a build error: uic was producing code that did not
-compile.
----
- src/plugins/external_tool_support/src/bowtie2/Bowtie2Settings.ui | 3 ---
- 1 file changed, 3 deletions(-)
-
---- src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-+++ src/plugins/external_tool_support/src/ui/Bowtie2Settings.ui
-@@ -254,9 +254,6 @@
-             <property name="text">
-              <string>Disallow gaps (--gbar)</string>
-             </property>
--            <property name="shortcut">
--             <string notr="true"/>
--            </property>
-            </widget>
-           </item>
-          </layout>
diff --git a/biology/ugene/files/patch-git_578c949 b/biology/ugene/files/patch-git_578c949
new file mode 100644
index 000000000000..8b11562770d1
--- /dev/null
+++ b/biology/ugene/files/patch-git_578c949
@@ -0,0 +1,25 @@
+From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001
+From: Yuliya Algaer <yalgaer@gmail.com>
+Date: Fri, 24 Aug 2018 21:24:12 +0700
+Subject: [PATCH] Build fix for Fedora
+
+--- src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
++++ src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
+@@ -20,6 +20,7 @@
+  */
+ 
+ #include <U2Core/U2SafePoints.h>
++#include <QIntValidator>
+ 
+ #include "LengthSettingsWidget.h"
+ #include "LineEditHighlighter.h"
+--- src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
++++ src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
+@@ -19,6 +19,7 @@
+  * MA 02110-1301, USA.
+  */
+ 
++#include <QIntValidator>
+ #include <U2Core/U2SafePoints.h>
+ 
+ #include "QualitySettingsWidget.h"
diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
index e75866cbf3c6..73f2d4038887 100644
--- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
+++ b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
@@ -1,4 +1,4 @@
---- src/corelibs/U2Private/U2Private.pro.orig	2016-03-31 12:22:14 UTC
+--- src/corelibs/U2Private/U2Private.pro.orig	2018-08-16 13:59:12 UTC
 +++ src/corelibs/U2Private/U2Private.pro
 @@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
             src/PluginSupportImpl.h \
@@ -14,7 +14,7 @@
  
  SOURCES += src/AppContextImpl.cpp \
             src/AppSettingsImpl.cpp \
-@@ -30,29 +25,7 @@ SOURCES += src/AppContextImpl.cpp \
+@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
             src/PluginSupportImpl.cpp \
             src/ServiceRegistryImpl.cpp \
             src/SettingsImpl.cpp \
@@ -26,22 +26,16 @@
 -           src/crash_handler/StackWalker.cpp
 +           src/TaskSchedulerImpl.cpp
  
- TRANSLATIONS += transl/english.ts \
-                 transl/russian.ts
--
--win32 {
--    HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
--    SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
+ TRANSLATIONS += transl/russian.ts
+ 
+ win32 {
+     HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
+     SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
 -}
 -
 -unix_not_mac() {
 -    HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
 -    SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
--}
--
--mac {
--    HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \
--               src/SleepPreventerMac.h
--    SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \
--               src/SleepPreventerMac.cpp
--}
+ }
+ 
+ mac {
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
new file mode 100644
index 000000000000..cc2164cb1db0
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
@@ -0,0 +1,22 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig	2018-09-02 00:22:54 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
+@@ -22,7 +22,7 @@
+ #include <cctype>
+ #include "GTKeyboardDriver.h"
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+     #define XK_LATIN1      // for latin symbol
+     #define XK_MISCELLANY  // for action keys
+     #include <X11/keysymdef.h>
+@@ -31,7 +31,7 @@
+ 
+ namespace HI {
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ 
+ #define GT_CLASS_NAME "GTKeyboardDriverLinux"
+ 
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
new file mode 100644
index 000000000000..8dfdd9b7d53f
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
@@ -0,0 +1,20 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig	2018-09-02 00:23:24 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp
+@@ -22,13 +22,13 @@
+ #include "GTMouseDriver.h"
+ #include <QByteArray>
+ 
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+     #include <X11/extensions/XTest.h>
+ #endif
+ 
+ namespace HI {
+ 
+-#ifdef __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ 
+ #define GT_CLASS_NAME "GTMouseDriver Linux"
+ QPoint GTMouseDriver::mousePos = QPoint(-1, -1);
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri b/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
deleted file mode 100644
index 3951d5f87ecb..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/libs_3rdparty/samtools/samtools.pri.orig	2016-03-31 12:21:56 UTC
-+++ src/libs_3rdparty/samtools/samtools.pri
-@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
- 
- TEMPLATE = lib
- CONFIG +=thread debug_and_release staticlib warn_off
--INCLUDEPATH += src src/samtools ../../include /usr/include
-+INCLUDEPATH += src src/samtools ../../include
- win32 : INCLUDEPATH += src/samtools/win32
- DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
- win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h b/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
deleted file mode 100644
index cf733a59a1de..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/plugins_3rdparty/phylip/src/phylip.h.orig	2017-12-30 19:54:56 UTC
-+++ src/plugins_3rdparty/phylip/src/phylip.h
-@@ -271,7 +271,6 @@ MALLOCRETURN    *mymalloc(long);
- #define MAXNCH          30   /* must be greater than or equal to nmlngth */
- #define maxcategs       9    /* maximum number of site types */
- #define maxcategs2     11    /* maximum number of site types + 2 */
--#define point           "."
- #define pointe          '.'
- #define down            2
- #define MAXSHIMOTREES 100
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp b/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
deleted file mode 100644
index 5a6131fbd06b..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp.orig	2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp
-@@ -28,9 +28,10 @@ namespace U2 {
- 
-     MuscleWorkPool::MuscleWorkPool(MuscleContext *_ctx, const MuscleTaskSettings  &_config, TaskStateInfo& _ti, int _nThreads, const MAlignment& _ma, MAlignment& _res, bool _mhack)
-         :ctx(_ctx), config(_config), ma(_ma), res(_res), mhack(_mhack), Weights(NULL), ProgNodes(NULL), ph(NULL), ti(_ti),
--        treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), ptrbOscillating(false), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
-+        treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0),
-         bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL)
-     {
-+            *ptrbOscillating = false;
-             refineConstructot();
-     }
-     MuscleWorkPool::~MuscleWorkPool() {
diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri b/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
deleted file mode 100644
index 9ecf2cc231fb..000000000000
--- a/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/plugins_3rdparty/variants/variants.pri.orig	2016-03-31 12:22:09 UTC
-+++ src/plugins_3rdparty/variants/variants.pri
-@@ -20,7 +20,7 @@ use_bundled_zlib() {
- win32 : LIBS += -lwsock32
- 
- 
--INCLUDEPATH += src ../../include /usr/include
-+INCLUDEPATH += src ../../include
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools 
- INCLUDEPATH += ../../libs_3rdparty/samtools/src
- INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools
diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
index 44f703d392b2..bd0d64942c01 100644
--- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
+++ b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
@@ -1,4 +1,4 @@
---- src/plugins_checker/src/Main.cpp.orig	2016-03-31 12:22:09 UTC
+--- src/plugins_checker/src/Main.cpp.orig	2018-08-16 13:59:06 UTC
 +++ src/plugins_checker/src/Main.cpp
 @@ -39,7 +39,7 @@
  #include <ServiceRegistryImpl.h>
@@ -20,7 +20,7 @@
  
      const char* build = QT_VERSION_STR, *runtime = qVersion();
      if (strcmp(build, runtime) > 0){
-@@ -140,7 +142,7 @@ int main(int argc, char **argv)
+@@ -141,7 +143,7 @@ int main(int argc, char **argv)
      delete cmdLineRegistry;
      appContext->setCMDLineRegistry(NULL);
  
diff --git a/biology/ugene/files/patch-src_ugene__globals.pri b/biology/ugene/files/patch-src_ugene__globals.pri
deleted file mode 100644
index 6c0a38639d38..000000000000
--- a/biology/ugene/files/patch-src_ugene__globals.pri
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/ugene_globals.pri.orig	2016-03-31 12:22:21 UTC
-+++ src/ugene_globals.pri
-@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA
- DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
- DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
- 
--unix : !macx : INCLUDEPATH-=/usr/include
--unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
-+#unix : !macx : INCLUDEPATH-=/usr/include
-+#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
- #unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH
- 
- # NGS package
diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
index e932d4efa4c9..917fc096b4c4 100644
--- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
+++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
@@ -1,6 +1,6 @@
---- src/ugenecl/src/Main.cpp.orig	2016-03-31 12:22:19 UTC
+--- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 UTC
 +++ src/ugenecl/src/Main.cpp
-@@ -94,7 +94,7 @@
+@@ -93,7 +93,7 @@
  #include <ServiceRegistryImpl.h>
  #include <SettingsImpl.h>
  #include <TaskSchedulerImpl.h>
@@ -9,7 +9,7 @@
  
  // local project imports
  #include "DumpHelpTask.h"
-@@ -192,9 +192,11 @@ static void setSearchPaths() {
+@@ -191,6 +191,7 @@ static void setSearchPaths() {
  
  int main(int argc, char **argv)
  {
@@ -17,10 +17,14 @@
      if (CrashHandler::isEnabled()) {
          CrashHandler::setupHandler();
      }
+@@ -198,6 +199,7 @@ int main(int argc, char **argv)
+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+         CrashHandler::setSendCrashReports(false);
+     }
 +#endif
+ 
      const char* build = QT_VERSION_STR, *runtime = qVersion();
      if (strcmp(build, runtime) > 0){
-         printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR);
 @@ -617,7 +619,7 @@ int main(int argc, char **argv)
      delete pwr;
      appContext->setAlignmentAlgorithmsRegistry(NULL);
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
index d968dad9c8d1..e5dcadcdea21 100644
--- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
+++ b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
@@ -1,6 +1,6 @@
---- src/ugeneui/src/Main.cpp.orig	2016-03-31 12:22:18 UTC
+--- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
 +++ src/ugeneui/src/Main.cpp
-@@ -134,7 +134,7 @@
+@@ -136,7 +136,7 @@
  #include <ServiceRegistryImpl.h>
  #include <SettingsImpl.h>
  #include <TaskSchedulerImpl.h>
@@ -9,7 +9,7 @@
  
  #include "app_settings/AppSettingsGUIImpl.h"
  #include "app_settings/logview_settings/LogSettingsGUIController.h"
-@@ -343,9 +343,11 @@ void fixMacFonts() {
+@@ -353,6 +353,7 @@ void fixMacFonts() {
  
  int main(int argc, char **argv)
  {
@@ -17,11 +17,15 @@
      if (CrashHandler::isEnabled()) {
          CrashHandler::setupHandler();
      }
+@@ -360,6 +361,7 @@ int main(int argc, char **argv)
+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+         CrashHandler::setSendCrashReports(false);
+     }
 +#endif
  
      QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
  
-@@ -966,7 +968,7 @@ int main(int argc, char **argv)
+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
      }
  
      UgeneUpdater::onClose();
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
index 7a76899e33f1..8962a9edc02e 100644
--- a/biology/ugene/files/patch-ugene.pro
+++ b/biology/ugene/files/patch-ugene.pro
@@ -1,4 +1,4 @@
---- ugene.pro.orig	2016-03-31 12:21:56 UTC
+--- ugene.pro.orig	2018-08-16 13:58:51 UTC
 +++ ugene.pro
 @@ -20,7 +20,6 @@ use_bundled_zlib() {
  }
@@ -7,19 +7,20 @@
 -          src/libs_3rdparty/breakpad \
            src/libs_3rdparty/qscore \
            src/libs_3rdparty/sqlite3 \
-           src/libs_3rdparty/gtest \
-@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s
+           src/libs_3rdparty/samtools \
+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
  win32 : UGENE_DEV_NULL = nul
  unix : UGENE_DEV_NULL = /dev/null
  
 -UGENE_LRELEASE =
--UGENE_LUPDATE = 
--system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = lrelease-qt5
--    UGENE_LUPDATE = lupdate-qt5
--} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = lrelease
--    UGENE_LUPDATE = lupdate
+-UGENE_LUPDATE =
+-message(Using QT from $$[QT_INSTALL_BINS])
+-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
+-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
 -}
 +UGENE_LRELEASE = $$LRELEASE
 +UGENE_LUPDATE = $$LUPDATE